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We had some disk corruption on our server, and after doing a fsck the database would not start. To get us back into production, I copied the postgres data folder, blew away the DB and restored from the latest pg_dump. But there is some data I'd love to retrieve from a specific table in the corrupted data folder.

When I try to start postgres using the corrupted data folder, it wouldn't start because of missing xlog files. So I used pg_resetxlog and it threw me another error: *missing pg_clog/0000*. I suspect that the file was lost during fsck fixes, so I copied that file over from my running server, and had to do the same for the *pg_stat_tmp* folder, and the *pg_multixact/offsets/0000* file.

Now postgres will start using the corrupted data folder, but when I psql into it, all the tables seem to be empty (row count 0). Some tables seem to be missing altogther and throws me an error: could not open file "base/16416661/16416776": No such file or directory

The table that I'm after though, seems to still exist, but it gives me a row count of 0, even though the file itself in the /base directory is 1Gb large.

I've also tried doing a pg_dump of the database, which gives me an empty file, and a dump of that specific table, which pg_dump says it can't find (it says the table doesn't exist, even though psql can see it)

Does anyone understand the internals of the /base files, and is there any way I can recover data from the database, or that single table?

1 Answer
1

First action

When facing corruption, before you do ANYTHING ELSE, take a complete file-system-level copy of the damaged database. See: http://wiki.postgresql.org/wiki/Corruption . Failure to do so destroys evidence about what caused the corruption, and means that if your repair efforts go badly and make things worse you can't undo them. Do not attempt any repair first.

You appear to have made the right choice an done that, assuming you really copied the whole datadir. However, you appear to have then messed with the copy. Before you do anything else, make a copy of that damaged datadir somewhere safe and do not touch it again. This is your hope of recovery. Never work on this copy - duplicate it, and test recovery attempts on the duplicate.

Don't trust that server!

BTW, I strongly recommend that you stop using this server:

We had some disk corruption on our server

is not ok. Until you know why that happened you should not be using that server. Retire it or put it aside and get some trustworthy hardware.

If you cannot do that, make absolutely certain you're doing at least daily logical backups and streaming replication with WAL archiving to a secondary server. Treat the faulty server as if it might vanish or eat your data again at any time.

If the disk corruption corresponded with a power failure, it's probably due to unsafe write-back caching or a system that's ignoring disk flush requests. This is why I do plug-pull testing on server deployments, and don't buy cheap SSDs.

Corruption cases tend to be somewhat unique and require lots of back-and-forth, so they're not usually a good fit for Stack Overflow.

Internal structure

As for the internals of the files in base/ ... you really need the system catalogs to interpret them usefully. The table structure is documented in PostgreSQL internals.

The structure of individual relation extents is basically a header, followed by a bunch of columns that're interpreted based on the system catalogs. If you've lost the system catalogs you've got no reliable way to tell what each column's type and name is, etc.

The other problem you have is that you've lost the transaction commit logs (pg_clog) that keep a record of open, commited, and rolled back transactions. With that data lost, you will need to do a dirty read of the tables in order to recover any data, because you no longer know which tuples were added by transactions that later rolled back, which are deleted, which are old versions of updated tuples, etc.

Recovery?

... will be very hard.

In theory you might be able to read the tuples out of the heap table extents. I am not aware of any tools to do this. You would need to be able to construct new system catalogs that matched the on-disk structure of the tables, probably with a stand-alone PostgreSQL backend (postgres --single).

I'd like it if PostgreSQL had better recovery options, but frankly, we prefer to have good backups and use streaming replication etc to avoid the need in the first place. Repairing DB corruption is always iffy and results in untrustworthy, mangled data. So in general - don't do that.

It might help if you still have a copy of your data directory from before you ran pg_resetxlog.

Prevention

excellent advice all around - thanks! I do have an untouched zipped copy of the data folder before I started messing around with it, so I try different things. But even that copy is missing required files - I think from the fsck and disk corruption. I'll definitely have to consider moving boxes, in the mean time we're taking more regular backups. Thanks again!
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jhchanJan 16 '14 at 17:16